Question: Tool for BAM coverage without the soft clipping base
0
gravatar for nayshool
23 months ago by
nayshool20
Israel
nayshool20 wrote:

Hi everyone,

I am looking for a software/script which calculate the mean coverage of an area without the soft clipping bases. It's exclude the soft/hard clipping bases and leave only the true annotated bases in the calculation.

thank you

coverage bam softclipping • 750 views
ADD COMMENTlink modified 23 months ago by Pierre Lindenbaum119k • written 23 months ago by nayshool20
0
gravatar for Devon Ryan
23 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Almost anything that produces coverage metrics will do what you're describing. As an example, you can use bamCoverage or multiBamSummary from deepTools to do this, though other common choices would be bedtools or even featureCounts.

ADD COMMENTlink written 23 months ago by Devon Ryan89k

I don't want to count the soft clipping reads. Are those software will not count them?

ADD REPLYlink written 23 months ago by nayshool20

Correct, none of those (or even samtools view -c) will count soft-clipped portions of reads.

ADD REPLYlink written 23 months ago by Devon Ryan89k
0
gravatar for Pierre Lindenbaum
23 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

GATK depthofcoverage: https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php

In most (all?) tools the clipping section is ignored.

ADD COMMENTlink written 23 months ago by Pierre Lindenbaum119k
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